I've been away and facing a mountain of work so I'll just
add a few tidbits here and then get back to you with more
re. Japan when I've got time to breathe.

Japan Rail passes are most definitely the way to go -
intercity and within Tokyo. As someone else said, you can
even use them for the trip from Narita airport into Tokyo
and JR also has a number of trains that are part of the rail
network within and around Tokyo. You won't be able to use JR
everywhere you want to go but.....for some areas it works.

You MUST buy your JR pass before you go to Japan - they
aren't available once you get there. As soon as you arrive
at Narita go to the JR office (downstairs on the way to the
train station itself) and they will give you a folded card
which is stamped with the date of issue and final date you
can use it. For in town travel you usually just show the man
at the service window your pass instead of putting an actual
ticket in the gate but for the Narita to Tokyo and intercity
travel you go to the JR office and buy tickets for the
specific dates and times that you want to travel (they'll
help you with scheduling - it's amazing how much a well-
oiled machine the transportation system is!). Don't even
consider paying the extra to get Green Car service - it's
really very little different than the normal service and
much more expensive.

I agree that it is worth your while spending some time
learning how to use chopsticks. Not only do some of the
smallest establishments not have cutlery but you'll enjoy
the BIG smile on your server's face when they offer you a
fork and you show them that you don't need it.

Toilets are very clean in Japan and the number of western-
style toilets has improved a great deal even since we lived
there in 1995 (we go back at least every other year). You'll
find most of the large washrooms (and those on trains) have
at least one cubicle devoted to westerners. But...if it
isn't ...you will have to perfect the "squat position"
which, by the way, is probably the most sanitary way to use
a public washroom anyway [as you said - apologies to anyone
who takes offense]!

Food courts in Japan are much more upscale than those in
Bangkok.

I have a website on Asia (with a lot on Japan) that is
dreadfully out of date and I'm afraid that many of the links
are dead now (but I have no time to update them) BUT, with
that as a caveat, you might find some useful information:
http://www.accomasia.com/japan.htm

Also - check the Zine archive because I (and others) have
written a lot about Japan over the last few years.